Contacts of the helix formed by residues 7 - 28 (chain 2) in PDB entry 1ILN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 7 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 SER* 1.3 75.8 - - - +
82 LYS* 1.4 71.9 + - - +
102 THR* 2.6 24.4 + - - -
112 GLN* 2.9 30.0 + - - +
1322 LEU* 4.1 3.8 - - - +
1332 THR* 2.7 42.6 + - + +
189B GLY 4.9 0.4 - - - +
190B GLU* 3.5 18.6 - - + +
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Residues in contact with LYS 8 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62 SER 4.2 5.4 - - - +
72 THR* 1.4 72.8 - - - +
92 LYS* 1.3 63.0 + - + +
102 THR 2.9 6.4 + - - -
112 GLN* 3.1 7.3 + - - +
122 LEU* 3.2 19.6 + - + +
132 GLN* 3.0 18.0 + - - -
190B GLU* 2.5 54.8 + - - +
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Residues in contact with LYS 9 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 SER 4.5 1.8 + - - -
72 THR 3.1 1.8 + - - -
82 LYS* 1.3 77.6 - - + +
102 THR* 1.4 58.1 + - - +
132 GLN* 2.5 40.9 + - - +
532 LEU* 4.2 8.4 - - + +
952 GLU* 2.6 29.2 + - - +
962 LEU* 4.1 10.6 + - - +
982 GLY* 5.8 4.7 - - - +
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Residues in contact with THR 10 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 SER 2.6 29.7 + - - +
72 THR 2.6 13.0 + - - -
82 LYS 3.4 0.9 - - - -
92 LYS* 1.4 79.1 - - - +
112 GLN* 1.3 57.1 - - - -
122 LEU 3.7 0.2 - - - -
132 GLN* 3.5 2.0 + - - +
142 LEU* 2.9 31.5 + - + +
532 LEU* 3.9 26.5 - - + -
962 LEU* 3.4 7.3 - - - +
1282 ILE* 5.0 8.5 - - + +
1322 LEU* 3.2 24.8 - - + +
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Residues in contact with GLN 11 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72 THR* 2.9 34.8 + - - +
82 LYS 4.6 0.2 - - - +
102 THR* 1.3 72.2 - - - +
122 LEU* 1.4 59.0 + - - +
132 GLN 2.9 5.3 + - - -
142 LEU* 4.2 4.5 - - - +
152 GLU* 2.8 35.5 + - + +
1282 ILE 5.5 1.6 - - - -
1292 ILE* 4.0 26.4 - - + +
1322 LEU* 5.2 4.3 - - + -
1332 THR* 2.7 48.2 + - - +
189B GLY* 2.7 35.8 + - - +
190B GLU* 4.9 0.4 - - - +
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Residues in contact with LEU 12 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 LYS* 3.2 22.6 + - + +
112 GLN* 1.4 73.8 - - - +
132 GLN* 1.4 65.2 + - - +
152 GLU* 3.1 16.3 - - - +
91B ARG* 2.6 45.6 + - + -
93B MET 3.6 3.5 - - - +
94B ALA* 3.7 20.6 - - + -
189B GLY* 3.7 9.6 - - - -
190B GLU* 3.4 39.0 - - + +
191B PHE* 6.2 2.5 - - + -
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Residues in contact with GLN 13 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82 LYS 3.0 21.4 + - - -
92 LYS* 2.5 43.8 + - - +
102 THR 3.7 0.4 - - - +
112 GLN 2.9 0.6 - - - -
122 LEU* 1.4 94.6 - - - +
142 LEU* 1.3 57.9 + - - +
152 GLU 3.2 2.0 - - - -
162 HIS* 2.8 28.6 + - - +
172 LEU 3.1 8.5 + - - -
922 ILE* 3.2 9.9 - - + +
952 GLU* 3.6 37.6 - - + +
962 LEU* 3.5 20.9 - - + -
91B ARG* 3.4 9.9 - - - +
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Residues in contact with LEU 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 THR* 2.9 21.8 + - - +
112 GLN* 3.1 1.5 + - - +
132 GLN* 1.3 77.6 - - - +
152 GLU* 1.4 58.2 + - - +
172 LEU* 3.0 23.8 + - + +
182 LEU* 3.0 29.3 + - - +
532 LEU* 4.3 14.8 - - + -
962 LEU* 3.7 17.0 - - + -
1242 PHE* 4.1 11.9 - - + -
1252 ALA* 3.7 31.6 - - + +
1282 ILE* 3.4 36.8 - - + +
1292 ILE* 3.7 11.9 - - + -
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Residues in contact with GLU 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112 GLN* 2.8 32.7 + - + +
122 LEU* 3.1 13.7 - - - +
142 LEU* 1.4 72.4 - - - +
162 HIS* 1.3 84.9 + - - +
182 LEU* 3.5 14.2 - - + +
192 LEU* 3.6 13.2 - - - +
1292 ILE* 3.5 28.5 - - + +
93B MET* 3.2 9.9 - - - +
94B ALA* 3.2 21.1 + - - +
188B GLN* 4.0 23.5 - - - +
189B GLY* 3.0 31.2 + - - +
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Residues in contact with HIS 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 GLN 2.8 10.4 + - - +
152 GLU* 1.3 86.2 + - - +
172 LEU* 1.4 65.4 + - - +
192 LEU* 2.9 19.3 + - - +
202 ASP* 3.5 18.9 + - - +
882 ASN* 4.1 21.9 + - + +
922 ILE* 3.7 18.8 - - + +
15B ARG* 4.6 6.2 + - - -
91B ARG* 4.2 11.9 - - + +
92B VAL* 4.2 13.3 - - + +
93B MET* 3.4 57.5 - - + +
134B TYR* 5.0 1.8 - + - -
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Residues in contact with LEU 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 GLN 3.1 2.0 + - - -
142 LEU* 3.0 19.6 + - + +
162 HIS* 1.4 78.6 - - - +
182 LEU* 1.3 65.0 + - - +
202 ASP* 2.8 18.0 + - - +
212 LEU* 3.1 38.3 + - + +
562 LEU* 5.3 2.5 - - + -
592 LEU* 4.6 5.6 - - + -
892 ILE* 3.6 24.2 - - + -
922 ILE* 3.6 29.4 - - + +
932 VAL* 3.7 19.3 - - + -
962 LEU* 3.4 27.6 - - + -
1242 PHE* 5.2 4.5 - - + -
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Residues in contact with LEU 18 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142 LEU 3.0 11.3 + - - +
152 GLU* 3.5 16.2 - - + +
172 LEU* 1.3 76.1 - - - +
192 LEU* 1.3 60.0 + - + +
212 LEU* 3.0 11.1 + - - +
222 GLN* 2.9 31.2 + - + +
1222 ILE* 3.7 24.5 - - + +
1252 ALA* 4.2 3.8 - - + +
1262 GLN* 3.4 43.3 - - + +
1292 ILE* 3.9 19.1 - - + -
174G LEU* 3.6 27.8 - - + -
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Residues in contact with LEU 19 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152 GLU 3.6 11.7 - - - +
162 HIS 2.9 10.7 + - - +
172 LEU 2.9 0.6 + - - -
182 LEU* 1.3 76.4 - - + +
202 ASP* 1.3 59.3 + - - +
222 GLN* 3.2 10.7 + - - +
232 MET* 2.8 31.6 + - - +
93B MET* 3.4 44.4 - - + -
134B TYR* 3.4 49.7 - - + +
135B PHE* 4.5 5.6 - - + -
188B GLN* 4.2 10.5 - - - +
174G LEU* 3.6 21.3 - - + -
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Residues in contact with ASP 20 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162 HIS* 3.5 21.1 + - - +
172 LEU* 2.8 6.3 + - - +
192 LEU* 1.3 75.1 - - - +
212 LEU* 1.4 58.9 + - - +
232 MET* 4.1 0.2 - - - +
242 ILE* 2.7 35.7 + - - +
852 LEU* 3.4 14.0 - - + +
882 ASN* 2.8 39.5 + - + +
892 ILE* 3.4 27.2 - - + +
134B TYR* 2.7 29.6 + - - -
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Residues in contact with LEU 21 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 LEU* 3.1 47.0 + - + +
182 LEU* 3.0 16.2 + - - +
202 ASP* 1.4 78.7 - - - +
222 GLN* 1.4 57.3 + - - +
242 ILE* 3.2 9.8 - - + +
252 LEU* 2.9 29.8 + - - +
592 LEU* 4.5 6.7 - - + -
892 ILE* 4.1 20.4 - - + -
1182 LEU* 4.5 7.1 - - + +
1212 TRP* 3.4 45.5 - - + +
1222 ILE* 3.5 16.5 - - + +
1242 PHE* 5.4 0.9 - - + -
1252 ALA* 4.1 3.8 - - + -
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Residues in contact with GLN 22 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182 LEU* 2.9 21.3 + - + +
192 LEU* 3.2 20.3 + - - +
212 LEU* 1.4 73.1 - - - +
232 MET* 1.3 72.4 + - - +
252 LEU* 3.2 0.7 + - - +
262 ASN* 2.8 36.6 + - - +
1222 ILE* 3.5 19.3 - - + +
133B HIS* 2.8 45.0 + - - -
134B TYR* 3.5 12.1 + - - +
161B LYS* 4.5 0.6 - - - +
174G LEU* 3.7 30.0 - - + +
175G CYS* 3.7 25.0 - - - +
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Residues in contact with MET 23 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192 LEU 2.8 16.7 + - - +
202 ASP 4.1 0.2 - - - +
222 GLN* 1.3 82.7 + - - +
242 ILE* 1.4 60.6 + - - +
262 ASN* 5.5 0.2 - - - +
272 GLY* 2.8 41.4 + - - -
782 PHE* 3.6 5.2 - - + -
792 HIS* 3.1 40.8 - - - +
802 LEU* 4.7 3.1 - - + -
852 LEU* 3.5 30.3 - - + -
133B HIS* 3.1 53.8 - - + -
134B TYR* 4.2 11.2 - - + +
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Residues in contact with ILE 24 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202 ASP 2.7 30.2 + - - +
212 LEU* 3.2 18.2 - - + +
232 MET* 1.4 73.0 - - - +
252 LEU* 1.4 58.1 + - - +
282 ILE* 2.8 54.9 + - + +
632 LEU* 5.7 3.8 - - + -
662 LEU* 5.5 0.9 - - + -
702 LEU* 4.1 17.3 - - + +
782 PHE* 4.2 1.8 - - + -
822 PRO* 6.0 0.9 - - + -
852 LEU* 3.7 26.2 - - + +
862 ILE* 5.2 9.9 - - + -
892 ILE* 3.8 13.5 - - + -
1182 LEU* 3.5 35.2 - - + -
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Residues in contact with LEU 25 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 LEU 2.9 19.7 + - - +
222 GLN 3.8 0.4 - - - +
242 ILE* 1.4 77.2 - - - +
262 ASN* 1.3 68.1 + - - +
282 ILE* 3.3 1.0 - - + +
292 ASN* 2.8 32.6 + - + +
1152 VAL* 3.5 32.5 - - + +
1182 LEU* 3.8 17.3 - - + -
1192 ASN* 3.6 22.4 - - - +
1222 ILE* 3.5 21.8 - - + -
175G CYS 4.3 0.4 - - - +
177G SER* 3.4 45.5 - - - +
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Residues in contact with ASN 26 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222 GLN 2.8 13.8 + - - +
252 LEU* 1.3 74.8 - - - +
272 GLY* 1.3 61.1 + - - +
292 ASN* 3.1 13.3 + - - -
302 ASN* 2.8 36.4 + - - +
772 ASN 5.2 0.8 + - - -
133B HIS* 4.3 16.1 - - + -
170G ARG* 5.6 1.6 + - - -
172G ASN* 4.7 4.3 - - - +
175G CYS* 3.5 38.7 + - + +
177G SER* 4.7 12.1 + - - -
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Residues in contact with GLY 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 MET* 2.8 42.7 + - - +
262 ASN* 1.3 74.8 - - - +
282 ILE* 1.4 58.8 + - - +
302 ASN* 3.2 2.8 + - - -
772 ASN* 2.8 37.8 + - - +
782 PHE* 3.5 12.8 - - - -
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Residues in contact with ILE 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 ILE* 2.8 48.6 + - + +
252 LEU* 3.3 9.2 - - + +
272 GLY* 1.4 72.7 - - - +
292 ASN* 1.3 76.4 + - + +
302 ASN 3.1 7.3 + - - +
332 ASN* 3.3 28.8 + - - +
362 LEU* 4.3 5.9 - - + +
702 LEU* 3.4 41.7 - - + +
732 ALA* 4.5 3.6 - - + -
782 PHE* 3.3 25.1 - - + -
1142 ILE* 4.3 21.5 - - + -
1152 VAL* 4.7 0.7 - - + -
1182 LEU* 4.2 10.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il